String Database: What Do "Conserved Neighborhood View" And "Co-Occurrence" Mean?

Question

[rezwan.02]

i can't understand the terms "Conserved Neighborhood View" & "Co-occurrence". what actually they mean and what are the use ?

Answer 1

[tevlon84]

Hi rezwan,

you can look up the definitions in the string-db manual : http://string-db.org/help/index.jsp?topic=/org.string-db.docs/howto.html

Conserved Neighborhood View

The neighborhood view shows runs of genes that occur repeatedly in close neighborhood in (prokaryotic) genomes. Genes located together in a run are linked with a black line (maximum allowed intergenic distance is 300 base pairs). Note that if there are multiple runs for a given species, these are separated by white space. If there are other genes in the run that are below the current score threshold, they are drawn as small white triangles. Gene fusion occurrences are also drawn, but only if they are present in a run (see also the Fusion section below for more details).

Co-occurrence

The occurrence view shows the presence or absence of linked proteins across species. Proteins are listed across the top of the page and a phylogenetic tree with species names is listed down the left hand side. In the subsequent grid, the presence of the protein in a species is marked with a red square and absence with a white space. The intensity of the color of the red square reflect the amount of conservation of the homologous protein in the specie.